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  1. IGB
  2. IGBF-3903

Add CRAM file format to the release testing documentation

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Critical
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Situation: We've recently added support for the CRAM file format to IGB.

          Task: Update the File Formats page of the IGB Release Documentation to include a test case for the CRAM file format.

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              pkulzer Paige Kulzer added a comment -

              I've added a CRAM section to the File Formats page which includes the name of the file to be added from the Smoke Testing Quickload, the chromosome and region to zoom to, and a picture of what IGB should look like at that region.

              Next steps: Add the CRAM file and its index to the Smoke Testing Quickload. Since the original CRAM file is quite large, I've subsetted it to only include a small region of chromosome 2 using samtools:

              samtools view -Cho NB72462M_HomoSapien.cram NB72462M.cram chr2:124,477,335-124,477,438
samtools index NB72462M_HomoSapien.cram

              I then checked the header to confirm that only the specified region was included (which it was):

              samtools view -H NB72462M_HomoSapien.cram
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              pkulzer Paige Kulzer added a comment - I've added a CRAM section to the File Formats page which includes the name of the file to be added from the Smoke Testing Quickload, the chromosome and region to zoom to, and a picture of what IGB should look like at that region. Next steps: Add the CRAM file and its index to the Smoke Testing Quickload. Since the original CRAM file is quite large, I've subsetted it to only include a small region of chromosome 2 using samtools: samtools view -Cho NB72462M_HomoSapien.cram NB72462M.cram chr2:124,477,335-124,477,438 samtools index NB72462M_HomoSapien.cram I then checked the header to confirm that only the specified region was included (which it was): samtools view -H NB72462M_HomoSapien.cram
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              nfreese Nowlan Freese added a comment - - edited

              The testing documentation looks good, and I was able to view the CRAM file.

              I have deployed the Cram file to the smoketesting S3 bucket used for release testing here: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/

              Closing ticket

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              nfreese Nowlan Freese added a comment - - edited The testing documentation looks good, and I was able to view the CRAM file. I have deployed the Cram file to the smoketesting S3 bucket used for release testing here: https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/ Closing ticket

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                • Assignee:
                  pkulzer Paige Kulzer
                  Reporter:
                  pkulzer Paige Kulzer
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